Genomic Analysis and Advanced Mining of Photorhabdus Isolates Reveal Cryptic Polyketide Synthase Clusters and Potent Anti-Staphylococcal Activity

This study investigates the genomic and antibacterial potential of five Photorhabdus isolates recovered from Heterorhabditis sp. entomopathogenic nematodes collected from soil samples in northern Thailand (Kamphaengphet and Phitsanulok provinces). Whole-genome sequencing combining Illumina short-read and Oxford Nanopore long-read platforms, followed by phylogenetic analysis, digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) calculations, classified strain KLK8.1 as Photorhabdus hainanensis and strains KLK18.5, NMP12.2, NMP13.3, and NMP13.5 as Photorhabdus akhurstii. Genome mining using antiSMASH v8.0 and DeepBGC v0.1.23 identified 134 biosynthetic gene clusters (BGCs) across the five genomes, including conserved clusters associated with symbiosis and a substantial proportion (~60%) of clusters lacking characterized homologs. Deep-learning-assisted mining further identified rare, highly reducing type II polyketide synthase (HR-T2PKS) clusters, which were predicted to be associated with polyene biosynthetic pathways. Antibacterial profiling by disc diffusion and minimum inhibitory concentration assays revealed that the crude extracts exhibited potent activity against Staphylococcus aureus and selective activity against Acinetobacter baumannii. These findings highlight the unexplored biosynthetic capacity of Thai Photorhabdus isolates and support their potential as valuable sources for discovering novel bioactive compounds.